MetNetComp Database [1] / Core Genes A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : ddca_p
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 573
  Remaining genes: STM0685 STM1203 STM4122 STM1473 STM2992 STM3901 STM3795 STM3796 STM3902 STM0320 STM0066 STM1883 STM1832 STM3190 STM4227 STM4230 STM4229 STM1831 STM4120 STM1712 STM2164 STM2162 STM2165 STM3468 STM0227 STM1067 STM2384 STM0623 STM1195 STM4273 STM2378 STM0060 STM0061 STM1197 STM0622 STM0059 STM0621 STM1198 STM1743 STM3469 STM1742 STM1824 STM1739 STM1745 STM1744 STM0812 STM0488 STM0165 STM1490 STM0203 STM0984 STM0207 STM3315 STM1196 STM1204 STM1342 STM0206 STM3158 STM1737 STM4130 STM0483 STM2811 STM2933 STM2809 STM1232 STM4366 STM0730 STM2953 s0001 STM3710 STM0232 STM3379 STM3173 STM3380 STM4121 STM2366 STM4176 STM0533 STM2430 STM0534 STM0154 STM0737 STM0736 STM3630 STM2432 STM2433 STM1464 STM2431 STM1557 STM3629 STM3628 STM3626 STM0130 STM0957 STM4340 STM0380 STM4342 STM0441 STM1802 STM0442 STM4343 STM0440 STM4247 STM0443 STM2555 STM2206 STM0934 STM1469 STM0761 STM3560 STM0980 STM3563 STM0762 STM3561 STM1468 STM4300 STM3013 STM3947 STM3562 STM3862 STM0222 STM3195 STM2095 STM3923 STM0202 STM4235 STM1347 STM3554 STM2670 STM0760 STM3555 STM3557 STM3740 STM3904 STM3700 STM2285 STM0064 STM2489 STM2284 STM0087 STM2365 STM1724 STM1723 STM3206 STM1058 STM0416 STM1163 STM0192 STM3295 STM0193 STM3486 STM1358 STM3719 STM1752 STM4123 STM1900 STM2098 STM2353 STM2190 STM2189 STM0889 STM0891 STM0887 STM2500 STM2352 STM0888 STM2351 STM3539 STM3861 STM4385 STM4384 STM3997 STM3877 STM3535 STM3722 STM3915 STM4459 STM2649 STM3718 STM3717 STM4460 STM4101 STM0002 STM1200 STM4220 STM2641 STM0998 STM0664 STM0663 STM0665 STM3692 STM1700 STM3713 STM3928 STM2071 STM3926 STM3866 STM3869 STM3867 STM3872 STM3865 STM3868 STM3871 STM1155 STM3864 STM3536 STM3870 STM4007 STM1889 STM0829 STM2458 STM0830 STM3314 STM4109 STM0330 STM1299 STM2362 STM4131 STM3331 STM0113 STM1777 STM2415 STM3909 STM0988 STM3316 STM1772 STM2947 STM0704 STM0705 STM3986 STM1695 STM3880 STM3053 STM3054 STM3055 STM3409 STM1570 STM4036 STM3655 STM1647 STM4037 STM1569 STM2167 STM4248 STM3200 STM0248 STM0592 STM0591 STM0594 STM2510 STM2199 STM0229 STM0191 STM0506 STM0585 STM2848 STM2852 STM2849 STM4285 STM2850 STM2847 STM1467 STM4084 STM1194 STM0045 STM0850 STM0848 STM0851 STM0152 STM2193 STM1711 STM2578 STM3359 STM4016 STM0171 STM3721 STM3716 STM3712 STM3711 STM3723 STM0844 STM3090 STM4115 STM3714 STM0246 STM4114 STM0843 STM0247 STM3965 STM3294 STM4221 STM2072 STM2074 STM1076 STM3938 STM0698 STM0183 STM0003 STM2820 STM0420 STM4182 STM2073 STM3724 STM1238 STM3715 STM1945 STM4063 STM2443 STM2252 STM0782 STM2254 STM0783 STM1337 STM2444 STM0781 STM2077 STM2441 STM2075 STM1725 STM2531 STM3903 STM3589 STM4105 STM3855 STM3856 STM2511 STM3854 STM3957 STM3390 STM2317 STM2321 STM2328 STM4414 STM2325 STM0112 STM2322 STM0329 STM2319 STM2320 STM0110 STM0111 STM2326 STM2324 STM2318 STM0372 STM2683 STM4119 STM2669 STM1310 STM2667 STM3076 STM1480 STM3823 STM1349 STM4175 STM2078 STM2487 STM3001 STM2526 STM0463 STM2565 STM2840 STM2076 STM4081 STM0645 STM1780 STM0978 STM0958 STM0145 STM4348 STM2259 STM2652 STM2255 STM2257 STM1727 STM2258 STM1726 STM1761 STM1577 STM1579 STM1578 STM0877 STM1762 STM0226 STM1226 STM1764 STM1225 STM0123 STM0879 STM2260 STM0880 STM0228 STM1222 STM3307 STM0128 STM0126 STM0129 STM4137 STM0865 STM3205 STM0756 STM1426 STM0417 STM0776 STM3474 STM0124 STM4279 STM3720 STM0134 STM4277 STM2817 STM4280 STM3883 STM3881 STM0218 STM2646 STM3884 STM0970 STM3936 STM3937 STM2278 STM1707 STM2807 STM2808 STM0535 STM2277 STM4451 STM0701 STM4452 STM3483 STM3114 STM4080 STM3733 STM1617 STM1933 STM3671 STM3672 STM3063 STM0386 STM0310 STM1710 STM0125 STM1893 STM2946 STM2934 STM2935 STM0153 STM2832 STM2834 STM4159 STM0425 STM4162 STM2483 STM2543 STM4161 STM0426 STM4469 STM0427 STM4465 STM0532 STM3699 STM4466 STM0429 STM3354 STM3477 STM3859 STM1269 STM2041 STM1359 STM2040 STM2043 STM2042 STM3401 STM3487 STM3147 STM0388 STM1539 STM0166 STM1786 STM2025 STM2020 STM2022 STM1788 STM2021 STM4100 STM0733 STM3624A STM0732 STM0735 STM0734 STM0738 STM0739 STM1498 STM2094 STM0965 STM2096 STM3922 STM4306 STM2097 STM0985 STM2528 STM0213 STM0609 STM2082 STM2085 STM2086 STM2087 STM2084 STM1497 STM2104 STM0108 STM0106 STM2083 STM2530 STM1332 STM3244 STM0964 STM3905 STM2092 STM2091 STM1496 STM2090 STM2093 STM0004 STM2089 STM2341 STM2340 STM2474 STM0434 STM2289 STM2573 STM2232 STM1793 STM0691 STM1314 STM0741 STM1312 STM1651 STM3253 STM0589 STM0054 STM3353 STM0055 STM3352 STM2786 STM2788 STM1377 STM1257 STM1255 STM1256 STM2838_S STM1258 STM3290_S STM3259 STM4188_S STM3260 STM2323_S STM3255 STM2316_S STM2864 STM2499_S STM1892_S STM2105_S STM2862 STM4305_S STM2863 STM1383 STM1385 STM2065 STM2064 STM2549 STM2550 STM2548   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.016290 (mmol/gDw/h)
  Minimum Production Rate : 0.257204 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.363357
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.190703
  EX_pi_e : 0.142987
  EX_k_e : 0.002893
  EX_so4_e : 0.001986
  EX_mg2_e : 0.000129
  EX_fe2_e : 0.000119
  EX_ca2_e : 0.000077
  EX_cl_e : 0.000077
  EX_cobalt2_e : 0.000051
  EX_cu2_e : 0.000051
  EX_mn2_e : 0.000051
  EX_mobd_e : 0.000051
  EX_zn2_e : 0.000051

Product: (mmol/gDw/h)
  EX_h2o_e : 11.247673
  EX_co2_e : 10.736987
  EX_dha_e : 4.975329
  EX_h_e : 0.425176
  Auxiliary production reaction : 0.257133
  EX_glyc3p_e : 0.128566
  EX_acald_e : 0.054335
  EX_4abz_e : 0.011190
  EX_ac_e : 0.009018
  EX_glyclt_e : 0.000815

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 27-Sep-2023
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